Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming

Distinct planting patterns exert legacy effects on the networks and assembly of root-associated microbiomes in subsequent crops

Soil legacy effects from previous crops can significantly influence plant-soil interactions in crop rotations. However, the microbial mechanism underlying this effect in subsequent root-associated compartments remains unclear. We investigated the effects of planting patterns (four-year continuous maize [MM], three-year winter wheat and one-year maize rotation [WM], and three-year potato and one-year maize rotation [PM]) on the microbial composition and structure of root-associated compartments, the effect of distinct crops on subsequent microbial co-occurrence patterns, and the assembly mechanism by which the root-associated compartments (bulk soil, rhizosphere, and roots) in subsequent crops regulate the microbiome habitat. Compared with MM, the relative abundance of Acidobacteria in WM was 29.7 % lower, whereas that of Bacteroidota in PM was 37.9 % higher in all three compartments. The co-occurrence patterns of the microbial communities exhibited varied responses to different planting patterns. Indicator taxon analysis revealed less shared and specific species in the root bacterial and fungal networks. The planting pattern elicited specific responses from modules within bacterial and fungal co-occurrence networks in all three compartments. Moreover, the planting patterns and root-associated compartments collectively drove the assembly process of root-associated microorganisms. The neutral model showed that, compared with MM, the stochasticity of bacterial assembly decreased under WM and PM but increased for fungal assembly. WM and PM increased the relative effects of the homogenized dispersal of fungal assemblies in roots. We conclude that previous crops exhibit marked legacy effects in the root-associated microbiome. Therefore, soil heritage should not be ignored when discussing microbiome recruitment strategies and co-occurrence patterns in subsequent crops.

Hydraulic conditions control the abundance of antibiotic resistance genes and their potential host microorganisms in a frequently regulated river-lake system

Antibiotic resistance genes (ARGs) are a growing problem that is widespread in river-lake ecosystems, where they pose a threat to the aquatic environment's health and public safety. These systems serve as critical nodes in water management, as they facilitate the equitable allocation of water resources through long-term and frequent water diversions. However, hydrological disturbances associated with water-regulation practices can influence the dynamics of their potential host microorganisms and associated resistance genes. Consequently, identifying the key ARGs and their resistance mechanisms in heavily regulated waters is vital for safeguarding human health and that of river-lake ecosystems. In this study, we examined the impact of water-regulation factors on ARGs and their hosts within a river-lake continuum using 16S rRNA and metagenomic sequencing. We found that a significant increase in ARG abundance during regulation periods (p < 0.05), especially in the aquatic environment. Key resistance genes were macB, tetA, evgS, novA, and msbA, with increased efflux pinpointed as their principal resistance mechanism. Network analysis identified Flavobacteriales, Acinetobacter, Pseudomonas, Burkholderiaceae, and Erythrobacter as key potential host microorganisms, which showed increased abundance within the water column during regulation periods (p < 0.05). Flow velocity and water depth both drove the host microorganisms and critical ARGs. Our findings underscore the importance of monitoring and mitigating the antibiotic resistance risk during water transfers in river-lake systems, thereby supporting informed management and conservation strategies.

The response patterns of r- and K-strategist bacteria to long-term organic and inorganic fertilization regimes within the microbial food web are closely linked to rice production

Soil microbial food web is crucial for maintaining crop production, while its community structure varies among fertilization regimes. Currently, the mechanistic understanding of the relationships between microbial food web and crop production under various nutrient fertilizations is poor. This knowledge gap limits our capacity to achieve precision agriculture for ensuring yield stability. In this study, we investigated the abiotic (i.e., soil chemical properties) and biotic factors (i.e., microbial food web, including bacteria, fungi, archaea and nematodes) that were closely associated with rice (Oryza sativa L.) production, using soils from seven fertilization regimes in distinct sampling locations (i.e., bulk vs rhizosphere soil) at a long-term experimental site. Organic manure alone fertilization (M) and integrated fertilization (NPKM) combining manure with inorganic fertilizers increased soil pH by 0.21-0.41 units and organic carbon content by 49.1 %-65.2 % relative to the non-fertilization (CK), which was distinct with inorganic fertilization. The principal coordinate analysis (PCoA) revealed that soil microbial and nematode communities were primarily shaped by fertilization rather than sampling locations. Organic fertilization (M, NPKM) increased the relative abundance of both r-strategist bacteria, specific taxa within the fungal (i.e., Pezizales) and nematode communities (i.e., omnivores-predators), whereas inorganic fertilization increased K-strategist bacteria abundances relative to the CK. Correspondingly, network analysis showed that the keystone taxa in the amplicon sequence variants (ASVs) enriched by organic manure and inorganic fertilization were mainly affiliated with r- and K-strategist bacteria, respectively. Structural equation modeling (SEM) analysis found that r- and K-strategist bacteria were positively correlated with rice production under organic and inorganic fertilization, respectively. Our results demonstrate that the response patterns of r/K-strategists to nutrient fertilization largely regulate rice yield, suggesting that the enhanced soil fertility and r-strategists contribute to the highest crop production in NPKM fertilization.

The effects of Pinus sylvestris L. geographical origin on the community and co-occurrence of fungal and bacterial endophytes in a common garden experiment

Below-ground microorganisms, particularly endophytes, are pivotal for plant establishment and functioning through nutrient acquisition and enhancing resistance to abiotic and biotic stresses. The impact of host plant origin within a species on the composition and interaction networks of root endophytic fungi and bacteria has been less explored compared with plant phylogeny and biological distance. This study investigates the effect of geographic origin on the fungal and bacterial microbiomes of Pinus sylvestris L. root endophytes. Roots from plants grown in a common garden, originating from six locations, were harvested in two distinct seasons. Fungal and bacterial microbiomes were analyzed using Illumina MiSeq sequencing. The operational taxonomic unit (OTU) richness of endophytic fungi and bacteria showed no significant variation due to tree origin or season. However, the Shannon diversity index for endophytic fungi was seasonally influenced. The composition of endophytic fungal and bacterial communities was affected by both tree origin and season, correlating with host root biochemical parameters, such as starch, total non-structural carbohydrates, carbon, nitrogen, and climatic factors, such as mean annual precipitation and temperature. Moreover, the abundance of specific endophytic fungi and bacteria varied across different P. sylvestris origins, depending on the season. The complexity of the co-occurrence networks of fungal and bacterial endophytes within P. sylvestris also differed by geographical origin and season. This study highlights the significant role of biochemical and climatic factors associated with tree origin in shaping interactions with endophytic communities, potentially affecting plant health and adaptability across diverse environments.

IMPORTANCE

This study advances our understanding of how plant ecotype and seasonal changes influence root endophytic communities in Scots pine (Pinus sylvestris). By examining trees from various origins grown in a common garden, it highlights the role of tree origin and season in shaping fungal and bacterial community and co-occurrence networks. Importantly, this research demonstrates that tree origin impacts the composition and interaction networks of root endophytes and depends on the season. The study's findings suggest that root biochemical traits and climatic conditions (e.g., temperature, precipitation) associated with tree origin are crucial in determining the assembly of endophytic communities. This understanding could lead to innovative strategies for enhancing plant health and adaptability across different environments, contributing to forestry and conservation efforts. The research underscores the complexity of plant-microbe interactions and the need for a comprehensive approach to studying them, highlighting the interplay between tree origin and microbial ecology in forest ecosystems.

Could flooding undermine progress in building climate-resilient crops?

Flooding threatens crop productivity, agricultural sustainability, and global food security. In this article I review the effects of flooding on plants and highlight three important gaps in our understanding: (i) effects of flooding on ecological interactions mediated by plants both below (changing root metabolites and exudates) and aboveground (changing plant quality and metabolites, and weakening the plant immune system), (ii) flooding impacts on soil health and microorganisms that underpin plant and ecosystems health, and (iii) the legacy impacts of flooding. Failure to address these overlooked aspects could derail and undermine the monumental progress made in building climate-resilient crops and soil-microbe-assisted plant resilience. Addressing the outlined knowledge gaps will enhance solutions developed to mitigate flooding and preserve gains made to date.

The plant-sucking insect selects assembly of the gut microbiota from environment to enhance host reproduction

Plant-sucking insects have intricate associations with a diverse array of microorganisms to facilitate their adaptation to specific ecological niches. The midgut of phytophagous true bugs is generally structured into four distinct compartments to accommodate their microbiota. Nevertheless, there is limited understanding regarding the origins of these gut microbiomes, the mechanisms behind microbial community assembly, and the interactions between gut microbiomes and their insect hosts. In this study, we conducted a comprehensive survey of microbial communities within the midgut compartments of a bean bug Riptortus pedestris, soybean plant, and bulk soil across 12 distinct geographical fields in China, utilizing high-throughput sequencing of the 16 S rRNA gene. Our findings illuminated that gut microbiota of the plant-sucking insects predominantly originated from the surrounding soil environment, and plants also play a subordinate role in mediating microbial acquisition for the insects. Furthermore, our investigation suggested that the composition of the insect gut microbiome was probably shaped by host selection and/or microbe-microbe interactions at the gut compartment level, with marginal influence from soil and geographical factors. Additionally, we had unveiled a noteworthy dynamic in the acquisition of core bacterial taxa, particularly Burkholderia, which were initially sourced from the environment and subsequently enriched within the insect midgut compartments. This bacterial enrichment played a significant role in enhancing insect host reproduction. These findings contribute to our evolving understanding of microbiomes within the insect-plant-soil ecosystem, shedding additional light on the intricate interactions between insects and their microbiomes that underpin the ecological significance of microbial partnerships in host adaptation.

Large scale exploration reveals rare taxa crucially shape microbial assembly in alkaline lake sediments

Alkaline lakes are extreme environments inhabited by diverse microbial extremophiles. However, large-scale distribution patterns, environmental adaptations, community assembly, and evolutionary dynamics of microbial communities remain largely underexplored. This study investigated the characteristics of microbial communities on rare and abundant taxa in alkaline lake sediments in west and northwest China. We observed that abundant taxa varied significantly with geographical distance, while rare taxa remained unaffected by regional differences. The assembly process of abundant taxa was influenced by dispersal limitation, whilst rare taxa were predominantly driven by heterogeneous selection. Network analysis indicated that rare taxa as core species for community interactions and community stability. Rare taxa exhibited higher speciation and transition rate than abundant taxa, serving as a genetic reservoir and potential candidates to become abundance taxa, highlighting their crucial role in maintaining microbial diversity. These insights underscore the significant influence of rare taxa on ecosystem biodiversity and stability in alkaline lakes.

Biogeographic and co-occurrence network differentiation of fungal communities in warm-temperate montane soils

Studying the biogeographic patterns of fungal communities across altitudinal and soil depth gradients is essential for understanding how environmental variations shape the diversity and functionality of these complex ecological assemblages. Here, we evaluated the response and assembly patterns of fungal communities to altitude and soil depth, and the co-occurrence patterns influencing soil fungal metabolic preferences on Dongling Mountain. We observed significant variations in fungal β-diversity, driven by elevation and soil depth, with climatic parameters (MAT and MAP) and nutrient concentrations (TOC, TP, and TN) serving as prominent influencers. Additionally, we found that the multiple substrate-induced respiration rate of fungi degrading various carbon substrates was diminished in high-altitude and subsurface soils compared to low-altitude and surface soils. Stochastic processes play a more important role in controlling fungal community assembly than deterministic processes, with dispersal limitation emerging as the main driver of community assembly. While greater network complexity was evident in the topsoil compared to the subsoil, both layers harbored altitude-sensitive OTUs (asOTUs) that belonging to distinct modules. Moreover, fungal groups sensitive to the same altitude exhibited similar metabolic preferences. The asOTUs designated for lower altitude areas favored unstable carbon substrates (glucose and sucrose), while those designated as higher altitude areas exhibited a preference for recalcitrant carbon (xylan and lignin). This evidence suggests that soil fungal communities respond to environmental changes by trading off their life strategies and metabolic characteristics.

Effects of vegetation degradation on soil microbial communities and ecosystem multifunctionality in a karst region, southwest China

Vegetation degradation caused by intense human disturbances poses a significant challenge to the preservation and improvement of ecosystem functions and services in the karst region of southwest China. Soil microorganisms are major regulators of ecosystem multifunctionality (EMF). Currently, there is a dearth of knowledge regarding the effects of vegetation degradation on soil microbial communities and their corresponding multiple ecosystem functions in karst regions. In this study, we selected the vegetation degradation sequences of second natural forest (NF), agroforestry (AS) and cropland (CL) to investigate the diversity of bacterial, fungal and protistan communities, and their hierarchical co-occurrence network, and EMF to explore the relationships between them. Compared to the NF, the carbon cycling index, nitrogen cycling index, soil water regulation power, and the EMF were significantly decreased by 8.2%-50.6%, 48.7%-86.8%, 19.8%-24.5%, and 31.4%-69.5% in the AS and CL, respectively. The development of EMF can be explained by the fungal, protistan and microbial hierarchical β-diversity, as well as the complexity (e.g. degree) of microbial hierarchical interactions during the process of vegetation degradation. Notably, correlations between the abundances of sensitive amplicon sequence variants (sASVs) for different karst vegetation types and EMF varied in distinct network modules, being positive in module 1 and negative in module 2. Moreover, the relative abundance of keystone taxa in fungal and protistan communities provided greater contributions to EMF than the bacterial communities. Additionally, random forest modeling showed that carbon and nitrogen sources, and soil water content, and trace elements (e.g. exchangeable magnesium, iron, manganese, and zinc) were identified as key driving factors of the EMF. Collectively, our findings demonstrate that vegetation degradation obviously alters soil microbial diversities and hierarchical interactions, emphasizing their key role in maintaining ecosystem functions and health in karst regions.

Enhancing intercropping sustainability: Manipulating soybean rhizosphere microbiome through cropping patterns

Understanding the responses of soybean rhizosphere and functional microbiomes in intercropping scenarios holds promise for optimizing nitrogen utilization in legume-based intercropping systems. This study investigated three cropping layouts under film mulching: sole soybean (S), soybean-maize intercropping in one row (IS), and soybean-maize intercropping in two rows (IIS), each subjected to two nitrogen levels: 110 kg N ha-1 (N110) and 180 kg N ha-1 (N180). Our findings reveal that cropping patterns alter bacterial and nifh communities, with approximately 5 % of soybean rhizosphere bacterial amplicon sequence variants (ASVs) and 42 % of rhizosphere nifh ASVs exhibiting altered abundances (termed sensitive ASVs). Root traits and soil properties shape these communities, with root traits exerting greater influence. Sensitive ASVs drive microbial co-occurrence networks and deterministic processes, predicting 85 % of yield variance and 78 % of partial factor productivity of nitrogen, respectively. These alterations impact bacterial and nifh diversity, complexity, stability, and deterministic processes in legume-based intercropping systems, enhancing performance in terms of yield, nitrogen utilization efficiency, land equivalent ratio, root nodule count, and nodule dry weight under IIS patterns with N110 compared to other treatments. Our findings underscore the importance of field management practices in shaping rhizosphere-sensitive ASVs, thereby altering microbial functions and ultimately impacting the productivity of legume-based intercropping systems. This mechanistic understanding of soybean rhizosphere microbial responses to intercropping patterns offers insights for sustainable intercropping enhancements through microbial manipulation.

Forest-to-Cropland Conversion Reshapes Microbial Hierarchical Interactions and Degrades Ecosystem Multifunctionality at a National Scale

Conversion from natural lands to cropland, primarily driven by agricultural expansion, could significantly alter soil microbiome worldwide; however, influences of forest-to-cropland conversion on microbial hierarchical interactions and ecosystem multifunctionality have not been fully understood. Here, we examined the effects of forest-to-cropland conversion on intratrophic and cross-trophic microbial interactions and soil ecosystem multifunctionality and further disclosed their underlying drivers at a national scale, using Illumina sequencing combined with high-throughput quantitative PCR techniques. The forest-to-cropland conversion significantly changed the structure of soil microbiome (including prokaryotic, fungal, and protistan communities) while it did not affect its alpha diversity. Both intrakingdom and interkingdom microbial networks revealed that the intratrophic and cross-trophic microbial interaction patterns generally tended to be more modular to resist environmental disturbance introduced from forest-to-cropland conversion, but this was insufficient for the cross-trophic interactions to maintain stability; hence, the protistan predation behaviors were still disturbed under such conversion. Moreover, key soil microbial clusters were declined during the forest-to-cropland conversion mainly because of the increased soil total phosphorus level, and this drove a great degradation of the ecosystem multifunctionality (by 207%) in cropland soils. Overall, these findings comprehensively implied the negative effects of forest-to-cropland conversion on the agroecosystem, from microbial hierarchical interactions to ecosystem multifunctionality.

Trade-offs in soil microbial functions and soil health in agroecosystems

Soil microbial communities play pivotal roles in maintaining soil health in agroecosystems. However, how the delivery of multiple microbial functions in agroecosystems is maintained remains poorly understood. This may put us at risk of incurring unexpected trade-offs between soil functions. We elucidate how interactions between soil microbes can lead to trade-offs in the functioning of agricultural soils. Interactions within soil microbial communities can result in not only positive but also neutral and negative relationships among soil functions. Altering soil conditions through soil health-improving agricultural management can alleviate these functional trade-offs by promoting the diversity and interrelationships of soil microbes, which can help to achieve more productive and sustainable agroecosystems.

Maize edible-legumes intercropping systems for enhancing agrobiodiversity and belowground ecosystem services

Intensification of staple crops through conventional agricultural practices with chemical synthetic inputs has yielded positive outcomes in food security but with negative environmental impacts. Ecological intensification using cropping systems such as maize edible-legume intercropping (MLI) systems has the potential to enhance soil health, agrobiodiversity and significantly influence crop productivity. However, mechanisms underlying enhancement of biological soil health have not been well studied. This study investigated the shifts in rhizospheric soil and maize-root microbiomes and associated soil physico-chemical parameters in MLI systems of smallholder farms in comparison to maize-monoculture cropping systems (MMC). Maize-root and rhizospheric soil samples were collected from twenty-five farms each conditioned by MLI and MMC systems in eastern Kenya. Soil characteristics were assessed using Black oxidation and Walkley methods. High-throughput amplicon sequencing was employed to analyze fungal and bacterial communities, predicting their functional roles and diversity. The different MLI systems significantly impacted soil and maize-root microbial communities, resulting in distinct microbe sets. Specific fungal and bacterial genera and species were mainly influenced and enriched in the MLI systems (e.g., Bionectria solani, Sarocladium zeae, Fusarium algeriense, and Acremonium persicinum for fungi, and Bradyrhizobium elkanii, Enterobacter roggenkampii, Pantoea dispersa and Mitsuaria chitosanitabida for bacteria), which contribute to nutrient solubilization, decomposition, carbon utilization, plant protection, bio-insecticides/fertilizer production, and nitrogen fixation. Conversely, the MMC systems enriched phytopathogenic microbial species like Sphingomonas leidyi and Alternaria argroxiphii. Each MLI system exhibited a unique composition of fungal and bacterial communities that shape belowground biodiversity, notably affecting soil attributes, plant well-being, disease control, and agroecological services. Indeed, soil physico-chemical properties, including pH, nitrogen, organic carbon, phosphorus, and potassium were enriched in MLI compared to MMC cropping systems. Thus, diversification of agroecosystems with MLI systems enhances soil properties and shifts rhizosphere and maize-root microbiome in favor of ecologically important microbial communities.

Leaf Health Status Regulates Endophytic Microbial Community Structure, Network Complexity, and Assembly Processes in the Leaves of the Rare and Endangered Plant Species Abies fanjingshanensis

The rare and endangered plant species Abies fanjingshanensis, which has a limited habitat, a limited distribution area, and a small population, is under severe threat, particularly due to poor leaf health. The plant endophytic microbiome is an integral part of the host, and increasing evidence indicates that the interplay between plants and endophytic microbes is a key determinant for sustaining plant fitness. However, little attention has been given to the differences in the endophytic microbial community structure, network complexity, and assembly processes in leaves with different leaf health statuses. Here, we investigated the endophytic bacterial and fungal communities in healthy leaves (HLs) and non-healthy leaves (NLs) of A. fanjingshanensis using 16S rRNA gene and internal transcribed spacer sequencing and evaluated how leaf health status affects the co-occurrence patterns and assembly processes of leaf endophytic microbial communities based on the co-occurrence networks, the niche breadth index, a neutral community model, and C-score metrics. HLs had significantly greater endophytic bacterial and fungal abundance and diversity than NLs, and there were significant differences in the endophytic microbial communities between HLs and NLs. Leaf-health-sensitive endophytic microbes were taxonomically diverse and were mainly grouped into four ecological clusters according to leaf health status. Poor leaf health reduced the complexity of the endophytic bacterial and fungal community networks, as reflected by a decrease in network nodes and edges and an increase in degrees of betweenness and assortativity. The stochastic processes of endophytic bacterial and fungal community assembly were weakened, and the deterministic processes became more important with declining leaf health. These results have important implications for understanding the ecological patterns and interactions of endophytic microbial communities in response to changing leaf health status and provide opportunities for further studies on exploiting plant endophytic microbes to conserve this endangered Abies species.

Divergent responses of rhizosphere soil phosphorus fractions and biological features of Salix psammophila to fertilization strategies under cadmium contamination

Soil oligotrophy in areas heavily contaminated with heavy metals poses a significant challenge to vegetation establishment and phytoremediation processes. Phosphorus (P) cycling plays a critical role in global biogeochemical cycles, but there is limited understanding of its response to varying fertilization strategies and its correlation with phytoremediation effectiveness. This study primarily investigated the effects of various fertilization strategies, including nitrogen (N, 300 mg·kg-1), P (100 mg·kg-1), NP (combined N and P at 300 mg·kg-1 and 100 mg·kg-1, respectively), and HP (high P, 300 mg·kg-1) application, on rhizosphere soil P fractions and P-solubilizing microbial community (harboring phoD and phoC genes, respectively) of Salix psammophila under cadmium contamination. Application of NP significantly enhanced plant growth and cadmium accumulation, whereas HP inhibited cadmium bioaccumulation but promoted its translocation. Compared to untreated soil, N application promoted P cycling, leading to increases of 141.9 %, 60.4 %, and 10.3 % in Resin-Pi, diluted HCl-Pi, and conc.HCl-Pi, respectively. P application decreased organic phosphorus (Po) fractions by 24.4 % - 225.8 %, but N incorporation mitigated the declining trend in Po and augmented alkaline phosphatase activity. Fertilization strategies significantly regulated phoC- or phoD-harboring bacterial community structure, but their differential nutrient demands resulted in distinct responses. The phoD-harboring bacteria exhibited higher diversity and network complexity, with numerous biomarkers and fertilizer-sensitive OTUs discovered across treatments. Structural equation modeling (SEM) analysis indicated that phytoremediation efficiency was directly affected by Pi fractions, and phoD-harboring bacteria exhibited stronger associations with Pi fractions than phoC-harboring bacteria. In conclusion, our results reveal potential pathways through which fertilization strategies influence phytoremediation by affecting the structure of P-solubilizing microbial community. Furthermore, our study emphasizes the importance of combined N and P application in promoting Cd accumulation in plants, with high P levels appearing as an ideal fertilization strategy for phytoremediation targeting the harvest of aboveground biomass.

Phages enhance both phytopathogen density control and rhizosphere microbiome suppressiveness

Bacteriophages, viruses that specifically target plant pathogenic bacteria, have emerged as a promising alternative to traditional agrochemicals. However, it remains unclear how phages should be applied to achieve efficient pathogen biocontrol and to what extent their efficacy is shaped by indirect interactions with the resident microbiota. Here, we tested if the phage biocontrol efficacy of Ralstonia solanacearum phytopathogenic bacterium can be improved by increasing the phage cocktail application frequency and if the phage efficacy is affected by pathogen-suppressing bacteria already present in the rhizosphere. We find that increasing phage application frequency improves R. solanacearum density control, leading to a clear reduction in bacterial wilt disease in both greenhouse and field experiments with tomato. The high phage application frequency also increased the diversity of resident rhizosphere microbiota and enriched several bacterial taxa that were associated with the reduction in pathogen densities. Interestingly, these taxa often belonged to Actinobacteria known for antibiotics production and soil suppressiveness. To test if they could have had secondary effects on R. solanacearum biocontrol, we isolated Actinobacteria from Nocardia and Streptomyces genera and tested their suppressiveness to the pathogen in vitro and in planta. We found that these taxa could clearly inhibit R. solanacearum growth and constrain bacterial wilt disease, especially when combined with the phage cocktail. Together, our findings unravel an undiscovered benefit of phage therapy, where phages trigger a second line of defense by the pathogen-suppressing bacteria that already exist in resident microbial communities.

IMPORTANCE

Ralstonia solanacearum is a highly destructive plant-pathogenic bacterium with the ability to cause bacterial wilt in several crucial crop plants. Given the limitations of conventional chemical control methods, the use of bacterial viruses (phages) has been explored as an alternative biological control strategy. In this study, we show that increasing the phage application frequency can improve the density control of R. solanacearum, leading to a significant reduction in bacterial wilt disease. Furthermore, we found that repeated phage application increased the diversity of rhizosphere microbiota and specifically enriched Actinobacterial taxa that showed synergistic pathogen suppression when combined with phages due to resource and interference competition. Together, our study unravels an undiscovered benefit of phages, where phages trigger a second line of defense by the pathogen-suppressing bacteria present in resident microbial communities. Phage therapies could, hence, potentially be tailored according to host microbiota composition to unlock the pre-existing benefits provided by resident microbiota.

Dissection of rhizosphere microbiome and exploiting strategies for sustainable agriculture

The rhizosphere microbiome plays critical roles in plant growth and provides promising solutions for sustainable agriculture. While the rhizosphere microbiome frequently fluctuates with the soil environment, recent studies have demonstrated that a small proportion of the microbiome is consistently assembled in the rhizosphere of a specific plant genotype regardless of the soil condition, which is determined by host genetics. Based on these breakthroughs, which involved exploiting the plant-beneficial function of the rhizosphere microbiome, we propose to divide the rhizosphere microbiome into environment-dominated and plant genetic-dominated components based on their different assembly mechanisms. Subsequently, two strategies to explore the different rhizosphere microbiome components for agricultural production are suggested, that is, the precise management of the environment-dominated rhizosphere microbiome by agronomic practices, and the elucidation of the plant genetic basis of the plant genetic-dominated rhizosphere microbiome for breeding microbiome-assisted crop varieties. We finally present the major challenges that need to be overcome to implement strategies for modulating these two components of the rhizosphere microbiome.

Harnessing root-soil-microbiota interactions for drought-resilient cereals

Cereal plants form complex networks with their associated microbiome in the soil environment. A complex system including variations of numerous parameters of soil properties and host traits shapes the dynamics of cereal microbiota under drought. These multifaceted interactions can greatly affect carbon and nutrient cycling in soil and offer the potential to increase plant growth and fitness under drought conditions. Despite growing recognition of the importance of plant microbiota to agroecosystem functioning, harnessing the cereal root microbiota remains a significant challenge due to interacting and synergistic effects between root traits, soil properties, agricultural practices, and drought-related features. A better mechanistic understanding of root-soil-microbiota associations could lead to the development of novel strategies to improve cereal production under drought. In this review, we discuss the root-soil-microbiota interactions for improving the soil environment and host fitness under drought and suggest a roadmap for harnessing the benefits of these interactions for drought-resilient cereals. These methods include conservative trait-based approaches for the selection and breeding of plant genetic resources and manipulation of the soil environments.

The interplay between the inoculation of plant growth-promoting rhizobacteria and the rhizosphere microbiome and their impact on plant phenotype

Microbial inoculation stands as a pivotal strategy, fostering symbiotic relationships between beneficial microorganisms and plants, thereby enhancing nutrient uptake, bolstering resilience against environmental stressors, and ultimately promoting healthier and more productive plant growth. However, while the advantageous roles of inoculants are widely acknowledged, the precise and nuanced impacts of inoculation on the intricate interactions of the rhizosphere microbiome remain significantly underexplored. This study explores the impact of bacterial inoculation on soil properties, plant growth, and the rhizosphere microbiome. By employing various bacterial strains and a synthetic community (SynCom) as inoculants in common bean plants, the bacterial and fungal communities in the rhizosphere were assessed through 16 S rRNA and ITS gene sequencing. Concurrently, soil chemical parameters, plant traits, and gene expression were evaluated. The findings revealed that bacterial inoculation generally decreased pH and V%, while increasing H+Al and m% in the rhizosphere. It also decreased gene expression in plants related to detoxification, photosynthesis, and defense mechanisms, while enhancing bacterial diversity in the rhizosphere, potentially benefiting plant health. Specific bacterial strains showed varied impacts on rhizosphere microbiome assembly, predominantly affecting rhizospheric bacteria more than fungi, indirectly influencing soil conditions and plants. Notably, Paenibacillus polymyxa inoculation improved plant nitrogen (by 5.2%) and iron levels (by 28.1%), whereas Bacillus cereus boosted mycorrhization rates (by 70%). Additionally, inoculation led to increased complexity in network interactions within the rhizosphere (∼15%), potentially impacting plant health. Overall, the findings highlight the significant impact of introducing bacteria to the rhizosphere, enhancing nutrient availability, microbial diversity, and fostering beneficial plant-microbe interactions.

Developing stable, simplified, functional consortia from Brachypodium rhizosphere for microbial application in sustainable agriculture

The rhizosphere microbiome plays a crucial role in supporting plant productivity and ecosystem functioning by regulating nutrient cycling, soil integrity, and carbon storage. However, deciphering the intricate interplay between microbial relationships within the rhizosphere is challenging due to the overwhelming taxonomic and functional diversity. Here we present our systematic design framework built on microbial colocalization and microbial interaction, toward successful assembly of multiple rhizosphere-derived Reduced Complexity Consortia (RCC). We enriched co-localized microbes from Brachypodium roots grown in field soil with carbon substrates mimicking Brachypodium root exudates, generating 768 enrichments. By transferring the enrichments every 3 or 7 days for 10 generations, we developed both fast and slow-growing reduced complexity microbial communities. Most carbon substrates led to highly stable RCC just after a few transfers. 16S rRNA gene amplicon analysis revealed distinct community compositions based on inoculum and carbon source, with complex carbon enriching slow growing yet functionally important soil taxa like Acidobacteria and Verrucomicrobia. Network analysis showed that microbial consortia, whether differentiated by growth rate (fast vs. slow) or by succession (across generations), had significantly different network centralities. Besides, the keystone taxa identified within these networks belong to genera with plant growth-promoting traits, underscoring their critical function in shaping rhizospheric microbiome networks. Furthermore, tested consortia demonstrated high stability and reproducibility, assuring successful revival from glycerol stocks for long-term viability and use. Our study represents a significant step toward developing a framework for assembling rhizosphere consortia based on microbial colocalization and interaction, with future implications for sustainable agriculture and environmental management.

Zonation of bulk and rhizosphere soil bacterial communities and their covariation patterns along the elevation gradient in riparian zones of three Gorges reservoir, China

Zonation is a typical pattern of soil distribution and species assembly across riparian habitats. Microorganisms are essential members of riparian ecosystems and whether soil microbial communities demonstrate similar zonation patterns and how bulk and rhizosphere soil microorganisms interact along the elevation (submergence stress) gradient remain largely unknown. In this study, bulk and rhizosphere (dominant plant) soil samples were collected and investigated across riparian zones where the submergence stress intensity increased as the elevation decreased. Results showed that the richness of bacterial communities in bulk and rhizosphere soil samples was significantly different and presented a zonation pattern along with the submergence stress gradient. Bulk soil at medium elevation that underwent moderate submergence stress had the most abundant bacterial communities, while the species richness of rhizobacteria at low elevation that experienced serious submergence stress was the highest. Additionally, principal coordinate analysis (PCoA) and significance tests showed that bulk and rhizosphere soil samples were distinguished according to the structure of bacterial communities, and so were bulk or rhizosphere soil samples from different elevations. Redundancy analysis (RDA) and Mantel test suggested that bacterial communities of bulk soil mainly relied on the contents of soil organic matter, total carbon (TC), total nitrogen (TN), sodium (Na), calcium (Ca) and magnesium (Mg). Contrastingly, the contents of Na and Mg were the main factors explaining the variation in rhizobacterial community composition. Correlation and microbial source tracking analyses showed thatthe relationship of bulk and rhizosphere soil bacteria became much stronger, and the rhizosphere soil may get more bacterial communities from bulk soil with the increase in submergence severity. Our results suggest that the abiotic and biotic components of the riparian ecosystem are closely covariant along the submergence stress gradient and imply that the bacterial community may be a key node linking soil physiochemical properties and vegetation communities.

Arbuscular mycorrhizal fungi and Streptomyces: brothers in arms to shape the structure and function of the hyphosphere microbiome in the early stage of interaction

BACKGROUND

Fungi and bacteria coexist in a wide variety of environments, and their interactions are now recognized as the norm in most agroecosystems. These microbial communities harbor keystone taxa, which facilitate connectivity between fungal and bacterial communities, influencing their composition and functions. The roots of most plants are associated with arbuscular mycorrhizal (AM) fungi, which develop dense networks of hyphae in the soil. The surface of these hyphae (called the hyphosphere) is the region where multiple interactions with microbial communities can occur, e.g., exchanging or responding to each other's metabolites. However, the presence and importance of keystone taxa in the AM fungal hyphosphere remain largely unknown.

RESULTS

Here, we used in vitro and pot cultivation systems of AM fungi to investigate whether certain keystone bacteria were able to shape the microbial communities growing in the hyphosphere and potentially improved the fitness of the AM fungal host. Based on various AM fungi, soil leachates, and synthetic microbial communities, we found that under organic phosphorus (P) conditions, AM fungi could selectively recruit bacteria that enhanced their P nutrition and competed with less P-mobilizing bacteria. Specifically, we observed a privileged interaction between the isolate Streptomyces sp. D1 and AM fungi of the genus Rhizophagus, where (1) the carbon compounds exuded by the fungus were acquired by the bacterium which could mineralize organic P and (2) the in vitro culturable bacterial community residing on the surface of hyphae was in part regulated by Streptomyces sp. D1, primarily by inhibiting the bacteria with weak P-mineralizing ability, thereby enhancing AM fungi to acquire P.

CONCLUSIONS

This work highlights the multi-functionality of the keystone bacteria Streptomyces sp. D1 in fungal-bacteria and bacterial-bacterial interactions at the hyphal surface of AM fungi. Video Abstract.

The Contributions of Sub-Communities to the Assembly Process and Ecological Mechanisms of Bacterial Communities along the Cotton Soil-Root Continuum Niche Gradient

Soil microbes are crucial in shaping the root-associated microbial communities. In this study, we analyzed the effect of the soil-root niche gradient on the diversity, composition, and assembly of the bacterial community and co-occurrence network of two cotton varieties. The results revealed that the bacterial communities in cotton soil-root compartment niches exhibited a skewed species abundance distribution, dominated by abundant taxa showing a strong spatial specificity. The assembly processes of the rhizosphere bacterial communities were mainly driven by stochastic processes, dominated by the enrichment pattern and supplemented by the depletion pattern to recruit bacteria from the bulk soil, resulting in a more stable bacterial community. The assembly processes of the endosphere bacterial communities were determined by processes dominated by the depletion pattern and supplemented by the enrichment pattern to recruit species from the rhizosphere, resulting in a decrease in the stability and complexity of the community co-occurrence network. The compartment niche shaped the diversity of the bacterial communities, and the cotton variety genotype was an important source of diversity in bacterial communities within the compartment niche. We suggest that the moderate taxa contribute to significantly more changes in the diversity of the bacterial community than the rare and abundant taxa during the succession of bacterial communities in the cotton root-soil continuum.

Soil prokaryotic and fungal biome structures associated with crop disease status across the Japan Archipelago

Archaea, bacteria, and fungi in the soil are increasingly recognized as determinants of agricultural productivity and sustainability. A crucial step for exploring soil microbiomes with important ecosystem functions is to perform statistical analyses on the potential relationship between microbiome structure and functions based on comparisons of hundreds or thousands of environmental samples collected across broad geographic ranges. In this study, we integrated agricultural field metadata with microbial community analyses by targeting 2,903 bulk soil samples collected along a latitudinal gradient from cool-temperate to subtropical regions in Japan (26.1-42.8 °N). The data involving 632 archaeal, 26,868 bacterial, and 4,889 fungal operational taxonomic units detected across the fields of 19 crop plant species allowed us to conduct statistical analyses (permutational analyses of variance, generalized linear mixed models, randomization analyses, and network analyses) on the relationship among edaphic factors, microbiome compositions, and crop disease prevalence. We then examined whether the diverse microbes form species sets varying in potential ecological impacts on crop plants. A network analysis suggested that the observed prokaryotes and fungi were classified into several species sets (network modules), which differed substantially in association with crop disease prevalence. Within the network of microbe-to-microbe coexistence, ecologically diverse microbes, such as an ammonium-oxidizing archaeon, an antibiotics-producing bacterium, and a potentially mycoparasitic fungus, were inferred to play key roles in shifts between crop-disease-promotive and crop-disease-suppressive states of soil microbiomes. The bird's-eye view of soil microbiome structure will provide a basis for designing and managing agroecosystems with high disease-suppressive functions.IMPORTANCEUnderstanding how microbiome structure and functions are organized in soil ecosystems is one of the major challenges in both basic ecology and applied microbiology. Given the ongoing worldwide degradation of agroecosystems, building frameworks for exploring structural diversity and functional profiles of soil microbiomes is an essential task. Our study provides an overview of cropland microbiome states in light of potential crop-disease-suppressive functions. The large data set allowed us to explore highly functional species sets that may be stably managed in agroecosystems. Furthermore, an analysis of network architecture highlighted species that are potentially used to cause shifts from disease-prevalent states of agroecosystems to disease-suppressive states. By extending the approach of comparative analyses toward broader geographic ranges and diverse agricultural practices, agroecosystem with maximized biological functions will be further explored.

Fungal, but not bacterial, diversity and network complexity promote network stability during roadside slope restoration

To restore degraded roadside ecosystems, conventional methods such as revegetation and soil amendment are frequently employed. However, our understanding of the long-term effects of these restoration approaches on soil microbial diversity and network complexity across different vegetation types remains poor, which contributes to poor restoration outcomes. In this study, we explored the effects of roadside slope restoration on microbial communities across different vegetation types at varying stages of restoration. We found that restoration time had a more pronounced impact on microbial diversity than specific vegetation type. As restoration progressed, microbial network complexity and fungal diversity increased, but bacterial diversity declined, suggesting that keystone taxa may contribute to network complexity. Interestingly, bacterial network complexity increased concomitant with decreasing network modularity and robustness, which may compromise system stability. Distinct vegetation types were associated with restoration-sensitive microbial communities at different restoration stages. Leguminouse and nitrogen-fixing plants, such as Albiziak alkora, Ginkgo biloba, Rhus chinensis, Rhapis excels, and Rubia cordifolia exhibited such associations after five years of restoration. These keystone taxa included Proteobacteria, Actinobacteria, Chloroflexi, Gemmatimonadota, and Myxococcota. We also found that bacterial alpha diversity was significantly correlated with restoration time, soil pH, moisture, available phosphate, nitrate nitrogen, and plant height, while fungal diversity was primarily shaped by restoration time. Together, our findings suggest that soil properties, environmental factors, vegetation type, and dominant species can be manipulated to guide the trajectory of ecological recovery by regulating the abundance of certain microbial taxa.

Diversity and assembly patterns of mangrove rhizosphere mycobiome along the Coast of Gazi Bay and Mida Creek in Kenya

Fungi are among key actors in the biogeochemical processes occurring in mangrove ecosystems. In this study, we investigated the changes of fungal communities in selected mangrove species by exploring differences in diversity, structure and the degree of ecological rearrangement occurring within the rhizospheres of four mangrove species (Sonneratia alba, Rhizophora mucronata, Ceriops tagal and Avicennia marina) at Gazi Bay and Mida Creek in Kenya. Alpha diversity investigation revealed that there were no significant differences in species diversity between the same mangrove species in the different sites. Rather, significant differences were observed in fungal richness for some of the mangrove species. Chemical parameters of the mangrove sediment significantly correlated with fungal alpha diversity and inversely with richness. The fungal community structure was significantly differentiated by mangrove species, geographical location and chemical parameters. Taxonomic analysis revealed that 96% of the amplicon sequence variants belonged to the Phylum Ascomycota, followed by Basidiomycota (3%). Predictive FUNGuild and co-occurrence network analysis revealed that the fungal communities in Gazi Bay were metabolically more diverse compared to those of Mida Creek. Overall, our results demonstrate that anthropogenic activities influenced fungal richness, community assembly and their potential ecological functions in the mangrove ecosystems investigated.

Impact of historical soil management on the interaction of plant-growth-promoting bacteria with maize (Zea mays L.)

Edaphic factors can modulate the effects of microbial inoculants on crop yield promotion. Given the potential complexity of microbial inoculant responses to diverse soil management practices, we hypothesize that sustainable management of soil and water irrigation may improve soil quality and enhance the effects of plant growth-promoting bacteria (PGPB). Consequently, the primary objective was to assess the effectiveness of microbial inoculants formulated with Herbaspirillum seropedicae (Hs) and Azospirillum brasilense (Ab) on maize growth in soils impacted by different historical conservation management systems. We evaluated two soil management systems, two irrigation conditions, and four treatments: T0 - without bioinoculant and 100% doses of NPK fertilization; T1 - Hs + humic substances and 40% of NPK fertilization; T2 - Ab and 40% of NPK fertilization; T3 - co-inoculation (Hs + Ab) and 40% of NPK fertilization. Using a reduced fertilization dose (40% NPK) associated with microbial inoculants proved efficient in increasing maize shoot dry mass : on average, there was a 16% reduction compared to the treatment with 100% fertilization. In co-inoculation (Hs + Ab), the microbial inoculants showed a mutualistic effect on plant response, higher than isolate ones, especially increasing the nitrogen content in no-tillage systems irrigated by swine wastewater. Under lower nutrient availability and higher biological soil quality, the microbial bioinputs positively influenced root development, instantaneous water use efficiency, stomatal conductance, and nitrogen contents.

Customized plant microbiome engineering for food security

Plant microbiomes play a vital role in promoting plant growth and resilience to cope with environmental stresses. Plant microbiome engineering holds significant promise to increase crop yields, but there is uncertainty about how this can best be achieved. We propose a step-by-step approach involving customized direct and indirect methods to condition soils and to match plants and microbiomes. Although three approaches, namely the development of (i) 'plant- and microbe-friendly' soils, (ii) 'microbe-friendly' plants, and (iii) 'plant-friendly' microbiomes, have been successfully tested in isolation, we propose that the combination of all three may lead to a step-change towards higher and more stable crop yields. This review aims to provide knowledge, future directions, and practical guidance to achieve this goal via customized plant microbiome engineering.

Enhancing soil health and strawberry disease resistance: the impact of calcium cyanamide treatment on soil microbiota and physicochemical properties

Introduction

Continuous strawberry cropping often causes soil-borne diseases, with 20 calcium cyanamide being an effective soil fumigant, pig manure can often be used as soil organic fertilizer. Its impact on soil microorganisms structure, however, remains unclear.

Methods

This study investigated the effectiveness of calcium cyanamide and pig manure in treating strawberry soil, specifically against strawberry anthracnose. We examined the physical and chemical properties of the soil and the rhizosphere microbiome and performed a network analysis.

Results

Results showed that calcium cyanamide treatment significantly reduces the mortality rate of strawberry in seedling stage by reducing pathogen abundance, while increasing actinomycetes and Alphaproteobacteria during the harvest period. This treatment also enhanced bacterial network connectivity, measured by the average connectivity of each Operational Taxonomic Unit (OTU), surpassing other treatments. Moreover, calcium cyanamide notably raised the levels of organic matter, available potassium, and phosphorus in the soil-key factors for strawberry disease resistance and yield.

Discussion

Overall, applying calcium cyanamide to soil used for continuous strawberry cultivation can effectively decrease anthracnose incidence. It may be by changing soil physical and chemical properties and enhancing bacterial network stability, thereby reducing the copy of anthracnose. This study highlights the dual benefit of calcium cyanamide in both disease control and soil nutrient enhancement, suggesting its potential as a valuable tool in sustainable strawberry farming.

Biochar application alters soil metabolites and nitrogen cycle-related microorganisms in a soybean continuous cropping system

Biochar application is a promising practice to enhance soil fertility. However, it is unclear how field-aged biochar affects the soil metabolites and microbial communities in soybean fields. Here, the rhizosphere soil performance after amending with biochar addition rates at 0 (CK), 20 (B20), 40 (B40), and 60 t ha-1 (B60) was examined via a five-year in-situ field experiment based on a soybean continuous cropping system. Untargeted metabolomics and metagenomics analysis techniques were applied to study the regulatory mechanism of biochar on soybean growth from metabolomics and N cycle microbiology perspectives. We found that the contents of soil total N (TN), available N (Ava N), NH4+-N, and NO3--N were significantly increased with biochar addition amounts by 20.0-65.7 %, 3.6-10.7 %, 29.5-57.1 %, and 24.4-46.7 %, respectively. The B20, B40, and B60 triggered 259 (236 were up-regulated and 23 were down-regulated), 236 (220 were up-regulated and 16 were down-regulated), and 299 (264 were up-regulated and 35 were down-regulated) differential metabolites, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis and topology analysis demonstrated that differential metabolites were highly enriched in seven metabolic pathways such as Oxidative phosphorylation and Benzoxazinoid biosynthesis. Moreover, ten differential metabolites were up-regulated in all three treatments with biochar. Biochar treatments decreased the Nitrospira abundance in soybean rhizosphere soil while increasing Bradyrhizobium abundance significantly in B60. Mantel test revealed that as the biochar addition rate grows, the correlation between Nitrospira and soil properties other than NO3--N became stronger. In conclusion, the co-application of biochar with fertilizers is a feasible and effective way to improve soil N supply, even though biochar has undergone field aging. This work offers new insights into the variations in soil metabolites and microbial communities associated with N metabolism processes under biochar addition in soybean continuous cropping soils.

Long-term push-pull cropping system shifts soil and maize-root microbiome diversity paving way to resilient farming system

BACKGROUND

The soil biota consists of a complex assembly of microbial communities and other organisms that vary significantly across farming systems, impacting soil health and plant productivity. Despite its importance, there has been limited exploration of how different cropping systems influence soil and plant root microbiomes. In this study, we investigated soil physicochemical properties, along with soil and maize-root microbiomes, in an agroecological cereal-legume companion cropping system known as push-pull technology (PPT). This system has been used in agriculture for over two decades for insect-pest management, soil health improvement, and weed control in sub-Saharan Africa. We compared the results with those obtained from maize-monoculture (Mono) cropping system.

RESULTS

The PPT cropping system changed the composition and diversity of soil and maize-root microbial communities, and led to notable improvements in soil physicochemical characteristics compared to that of the Mono cropping system. Distinct bacterial and fungal genera played a crucial role in influencing the variation in microbial diversity within these cropping systems. The relative abundance of fungal genera Trichoderma, Mortierella, and Bionectria and bacterial genera Streptomyces, RB41, and Nitrospira were more enriched in PPT. These microbial communities are associated with essential ecosystem services such as plant protection, decomposition, carbon utilization, bioinsecticides production, nitrogen fixation, nematode suppression, phytohormone production, and bioremediation. Conversely, pathogenic associated bacterial genus including Bryobacter were more enriched in Mono-root. Additionally, the Mono system exhibited a high relative abundance of fungal genera such as Gibberella, Neocosmospora, and Aspergillus, which are linked to plant diseases and food contamination. Significant differences were observed in the relative abundance of the inferred metabiome functional protein pathways including syringate degradation, L-methionine biosynthesis I, and inosine 5'-phosphate degradation.

CONCLUSION

Push-pull cropping system positively influences soil and maize-root microbiomes and enhances soil physicochemical properties. This highlights its potential for agricultural and environmental sustainability. These findings contribute to our understanding of the diverse ecosystem services offered by this cropping system where it is practiced regarding the system's resilience and functional redundancy. Future research should focus on whether PPT affects the soil and maize-root microbial communities through the release of plant metabolites from the intercrop root exudates or through the alteration of the soil's nutritional status, which affects microbial enzymatic activities.

Exploring ecological effects of arsenic and cadmium combined exposure on cropland soil: from multilevel organisms to soil functioning by multi-omics coupled with high-throughput quantitative PCR

Arsenic (As) and cadmium (Cd) pose potential ecological threats to cropland soils; however, few studies have investigated their combined effects on multilevel organisms and soil functioning. Here, we used collembolans and soil microbiota as test organisms to examine their responses to soil As and Cd co-contamination at the gene, individual, and community levels, respectively, and further uncovered ecological relationships between pollutants, multilevel organisms, and soil functioning. At the gene level, collembolan transcriptome revealed that elevated As concentrations stimulated As-detoxifying genes AS3MT and GST, whereas the concurrent Cd restrained GST gene expression. At the individual level, collembolan reproduction was sensitive to pollutants while collembolan survival wasn't. At the community level, significant but inconsistent correlations were observed between the biodiversity of different soil keystone microbial clusters and soil As levels. Moreover, soil functioning related to nutrient (e.g., carbon, nitrogen, phosphorus, and sulfur) cycles was inhibited under As and Cd co-exposure only through the mediation of plant pathogens. Overall, these findings suggested multilevel bioindicators (i.e., AS3MT gene expression in collembolans, collembolan reproduction, and biodiversity of soil keystone microbial clusters) in cropland soils co-contaminated with As and Cd, thus improving the understanding of the ecotoxicological impact of heavy metal co-contamination on soil ecosystems.

Organic farming promotes the abundance of fungi keystone taxa in bacteria-fungi interkingdom networks

Soil bacteria-fungi interactions are essential in the biogeochemical cycles of several nutrients, making these microbes major players in agroecosystems. While the impact of the farming system on microbial community composition has been extensively reported in the literature, whether sustainable farming approaches can promote associations between bacteria and fungi is still unclear. To study this, we employed 16S, ITS, and 18S DNA sequencing to uncover how microbial interactions were affected by conventional and organic farming systems on maize crops. The Bray-Curtis index revealed that bacterial, fungal, and arbuscular mycorrhizal fungi communities were significantly different between the two farming systems. Several taxa known to thrive in healthy soils, such as Nitrosophaerales, Orbiliales, and Glomus were more abundant in the organic farming system. Constrained ordination revealed that the organic farming system microbial community was significantly correlated with the β-glucosidase activity, whereas the conventional farming system microbial community significantly correlated with soil pH. Both conventional and organic co-occurrence interkingdom networks exhibited a parallel node count, however, the former had a higher number of edges, thus being denser than the latter. Despite the similar amount of fungal nodes in the co-occurrence networks, the organic farming system co-occurrence network exhibited more than 3-fold the proportion of fungal taxa as keystone nodes than the conventional co-occurrence network. The genera Bionectria, Cercophora, Geastrum, Penicillium, Preussia, Metarhizium, Myceliophthora, and Rhizophlyctis were among the fungal keystone nodes of the organic farming system network. Altogether, our results uncover that beyond differences in microbial community composition between the two farming systems, fungal keystone nodes are far more relevant in the organic farming system, thus suggesting that bacteria-fungi interactions are more frequent in organic farming systems, promoting a more functional microbial community.

Farmland Microhabitat Mediated by a Residual Microplastic Film: Microbial Communities and Function

How the plastisphere mediated by the residual microplastic film in farmlands affects microhabitat systems is unclear. Here, microbial structure, assembly, and biogeochemical cycling in the plastisphere and soil in 33 typical farmland sites were analyzed by amplicon sequencing of 16S rRNA genes and ITS and metagenome analysis. The results indicated that residual microplastic film was colonized by microbes, forming a unique niche called the plastisphere. Notable differences in the microbial community structure and function were observed between soil and plastisphere. Residual microplastic film altered the microbial symbiosis and assembly processes. Stochastic processes significantly dominated the assembly of the bacterial community in the plastisphere and soil but only in the plastisphere for the fungal community. Deterministic processes significantly dominated the assembly of fungal communities only in soil. Moreover, the plastisphere mediated by the residual microplastic film acted as a preferred vector for pathogens and microorganisms associated with plastic degradation and the nitrogen and sulfur cycle. The abundance of genes associated with denitrification and sulfate reduction activity in the plastisphere was pronouncedly higher than that of soil, which increase the potential risk of nitrogen and sulfur loss. The results will offer a scientific understanding of the harm caused by the residual microplastic film in farmlands.

The microbial contribution to litter decomposition and plant growth

Soil and plant roots are colonized by highly complex and diverse communities of microbes. It has been proposed that bacteria and fungi have synergistic effects on litter decomposition, but experimental evidence supporting this claim is weak. In this study, we manipulated the composition of two microbial kingdoms (Bacteria and Fungi) in experimental microcosms. In microcosms that were inoculated with fungi, litter loss was 47% higher than in microcosms that were not inoculated or only inoculated with bacteria. Combined inoculation with both bacteria and fungi did not significantly enhance decomposition compared with the fungi-only treatments, and, as such, we found no evidence for complementary effects using our experimental setup. Inoculation with fungi also had a positive impact on plant growth after 4 and 8 weeks (480% and 710% growth stimulation, respectively). After 16 weeks, plant biomass was highest in microcosms where both bacteria and fungi were present pointing to fungal-bacterial complementarity in stimulating plant growth. Overall, this study suggests that fungi are the main decomposers of plant litter and that the inoculated fungi contribute to plant growth in our experimental system.

A tripartite bacterial-fungal-plant symbiosis in the mycorrhiza-shaped microbiome drives plant growth and mycorrhization

BACKGROUND

Plant microbiomes play crucial roles in nutrient cycling and plant growth, and are shaped by a complex interplay between plants, microbes, and the environment. The role of bacteria as mediators of the 400-million-year-old partnership between the majority of land plants and, arbuscular mycorrhizal (AM) fungi is still poorly understood. Here, we test whether AM hyphae-associated bacteria influence the success of the AM symbiosis.

RESULTS

Using partitioned microcosms containing field soil, we discovered that AM hyphae and roots selectively assemble their own microbiome from the surrounding soil. In two independent experiments, we identified several bacterial genera, including Devosia, that are consistently enriched on AM hyphae. Subsequently, we isolated 144 pure bacterial isolates from a mycorrhiza-rich sample of extraradical hyphae and isolated Devosia sp. ZB163 as root and hyphal colonizer. We show that this AM-associated bacterium synergistically acts with mycorrhiza on the plant root to strongly promote plant growth, nitrogen uptake, and mycorrhization.

CONCLUSIONS

Our results highlight that AM fungi do not function in  isolation and that the plant-mycorrhiza symbiont can recruit beneficial bacteria that support the symbiosis. Video Abstract.

Soil quality and microbial communities in subtropical slope lands under different agricultural management practices

Land degradation is a major threat to ecosystem. Long-term conventional farming practices can lead to severe soil degradation and a decline in crop productivity, which are challenging for both local and global communities. This study was conducted to clarify the responses on soil physicochemical properties and microbial communities to changes in farming practices. Slope land orchards under three agricultural management practices-conventional farming (CF), organic farming (OF), and ecofriendly farming (EFF)-were included in this study. We found that soil carbon stock increased by 3.6 and 5.1 times in surface soils (0-30 cm) under EFF and OF treatments, respectively. EFF and OF significantly increased the contents of total nitrogen by 0.33-0.46 g/kg, ammonia-N by 3.0-7.3 g/kg, and microbial biomass carbon by 0.56-1.04 g/kg but reduced those of pH by 0.6 units at least, and available phosphorous by 104-114 mg/kg. The application of phosphorous-containing herbicides and chemical fertilizers might increase the contents of phosphorous and nitrate in CF soil. High abundances of Acidobacteria and Actinobacteria were observed in EFF and OF soils, likely because of phosphorous deficiency in these soils. The abundance of fungi in OF soil indicated that plants' demand for available soil phosphorous induced the fungus-mediated mineralization of organic phosphorous. High abundances of Gammaproteobacteria, Planctomycetes, Firmicutes, and Nitrospirae were observed in CF soil, possibly because of the regular use of herbicides containing phosphorous and chemical fertilizers containing high total nitrogen contents.

Spatio-temporal distribution and dynamics of antibiotic resistance genes in a water-diversion lake, China

The distribution and dynamics of antibiotic resistance genes (ARGs) in water-diversion lakes are poorly understood. In this study, two comparative in situ investigations of ARG profiles targeting water diversion (DP) and non-diversion periods (NDP) were conducted in Luoma Lake, a vital transfer node for the eastern route of the South-to-North Water Diversion Project in China. The results demonstrated significant spatiotemporal variations in ARG contamination and notable differences in the co-occurrence patterns of ARGs and bacterial communities between DP and NDP. Correlations among ARGs with the 16 S rRNA, and mobile genetic elements indicate that horizontal gene transfer (HGT) and vertical gene transfer (VGT) in NDP, but only HGT in DP, were the primary mechanisms of ARG proliferation and spread, implying that water diversion could be an essential control of the transfer pattern of ARGs in a lake environment. The null model analysis indicated that stochastic processes, with predominant driver of ecological drift in the lake mainly drove the assembly of ARGs. Partial least squares structural equation modeling was developed to analyze the causal effects of the factors in shaping ARG dynamics and identify the major driving forces in the DP and NDP.

Deciphering key factors in pathogen-suppressive microbiome assembly in the rhizosphere

In a plant-microbe symbiosis, the host plant plays a key role in promoting the association of beneficial microbes and maintaining microbiome homeostasis through microbe-associated molecular patterns (MAMPs). The associated microbes provide an additional layer of protection for plant immunity and help in nutrient acquisition. Despite identical MAMPs in pathogens and commensals, the plant distinguishes between them and promotes the enrichment of beneficial ones while defending against the pathogens. The rhizosphere is a narrow zone of soil surrounding living plant roots. Hence, various biotic and abiotic factors are involved in shaping the rhizosphere microbiome responsible for pathogen suppression. Efforts have been devoted to modifying the composition and structure of the rhizosphere microbiome. Nevertheless, systemic manipulation of the rhizosphere microbiome has been challenging, and predicting the resultant microbiome structure after an introduced change is difficult. This is due to the involvement of various factors that determine microbiome assembly and result in an increased complexity of microbial networks. Thus, a comprehensive analysis of critical factors that influence microbiome assembly in the rhizosphere will enable scientists to design intervention techniques to reshape the rhizosphere microbiome structure and functions systematically. In this review, we give highlights on fundamental concepts in soil suppressiveness and concisely explore studies on how plants monitor microbiome assembly and homeostasis. We then emphasize key factors that govern pathogen-suppressive microbiome assembly. We discuss how pathogen infection enhances plant immunity by employing a cry-for-help strategy and examine how domestication wipes out defensive genes in plants experiencing domestication syndrome. Additionally, we provide insights into how nutrient availability and pH determine pathogen suppression in the rhizosphere. We finally highlight up-to-date endeavors in rhizosphere microbiome manipulation to gain valuable insights into potential strategies by which microbiome structure could be reshaped to promote pathogen-suppressive soil development.

Comprehensive profiling and risk assessment of antibiotic resistance genes in a drinking water watershed by integrated analysis of air-water-soil

The prevalence of antibiotic resistance genes (ARGs) in diverse habitats threatens public health. Watersheds represent critical freshwater ecosystems that interact with both the soil and atmosphere. However, a holistic understanding of ARGs distribution across these environmental media is currently inadequate. We profiled ARGs and bacterial communities in air-water-soil in the same watershed area during four seasons using high-throughput qPCR and 16S rRNA gene sequencing. Our findings demonstrated that aminoglycoside resistance genes (58.5%) were dominant in water, and multidrug resistance genes (55.2% and 54.2%) were dominant in soil and air. Five ARGs and nineteen bacterial genera were consistently detected in all samples, were named as shared genes or bacteria. Co-occurrence Network analysis revealed the co-occurrence module of resistance genes, mobile genetic elements (MGEs), and potential bacterial hosts, indicating that shared genes and bacteria may persist and co-spread across different environmental media. The risk assessment framework, based on ARGs' abundance, detection rate, and mobility, identified 33 high-risk ARGs. This is essential to evaluate the health risks of ARGs and to develop strategies to limit the threat of antibiotic resistance. Our study offers new insights into the risks associated with ARGs in the environment and suggests that ARGs may depend on specific bacterial cohabitants that co-exist with MGEs to facilitate their spread across environmental interfaces.

Potentilla parvifolia strongly influenced soil microbial community and environmental effect along an altitudinal gradient in central Qilian Mountains in western China

The Qilian Mountains (QLMs) form an important ecological security barrier in western China and a priority area for biodiversity conservation. Potentilla parvifolia is a widespread species in the mid-high altitudes of the QLMs and has continuously migrated to higher altitudes in recent years. Understanding the effects of P. parvifolia on microbial community characteristics is important for exploring future changes in soil biogeochemical processes in the QLMs. This study found that P. parvifolia has profound effects on the community structure and ecological functions of soil microorganisms. The stability and complexity of the root zone microbial co-occurrence network were significantly higher than those of bare soils. There was a distinct altitudinal gradient in the effect of P. parvifolia on soil microbial community characteristics. At an elevation of 3204 m, P. parvifolia promoted the accumulation of carbon, nitrogen, and phosphorus and increased sucrase activity and soil C/N while significantly improving the community richness index of fungi (p < .05) compared with that of bacteria and the relative abundance of Ascomycota. The alpha diversity of fungi in the root zone soil of P. parvifolia was also significantly increased at 3550 m altitude. Furthermore, the community similarity distance matrix of fungi showed an evident separation at 3204 m. However, at an altitude of 3750 m, P. parvifolia mainly affected the bacterial community. Potentilla parvifolia increased the bacterial community richness. This is in agreement with the findings based on the functional prediction that P. parvifolia favors the growth and enrichment of denitrifying communities at 3550 and 3750 m. The results provide a scientific basis for predicting the evolutionary trends of the effects of P. parvifolia on soil microbial communities and functions and have important implications for ecological governance in the QLMs.

Agricultural tillage practice and rhizosphere selection interactively drive the improvement of soybean plant biomass

Rhizosphere microbes play key roles in plant growth and productivity in agricultural systems. One of the critical issues is revealing the interaction of agricultural management (M) and rhizosphere selection effects (R) on soil microbial communities, root exudates and plant productivity. Through a field management experiment, we found that bacteria were more sensitive to the M × R interaction effect than fungi, and the positive effect of rhizosphere bacterial diversity on plant biomass existed in the bacterial three two-tillage system. In addition, inoculation experiments demonstrated that the nitrogen cycle-related isolate Stenotrophomonas could promote plant growth and alter the activities of extracellular enzymes N-acetyl- d-glucosaminidase and leucine aminopeptidase in rhizosphere soil. Microbe-metabolites network analysis revealed that hubnodes Burkholderia-Caballeronia-Paraburkholderia and Pseudomonas were recruited by specific root metabolites under the M × R interaction effect, and the inoculation of 10 rhizosphere-matched isolates further proved that these microbes could promote the growth of soybean seedlings. Kyoto Encyclopaedia of Genes and Genomes pathway analysis indicated that the growth-promoting mechanisms of these beneficial genera were closely related to metabolic pathways such as amino acid metabolism, melatonin biosynthesis, aerobactin biosynthesis and so on. This study provides field observation and experimental evidence to reveal the close relationship between beneficial rhizosphere microbes and plant productivity under the M × R interaction effect.

Peanut-based Rotation Stabilized Diazotrophic Communities and Increased Subsequent Wheat Yield

The introduction of legumes into rotations can improve nitrogen use efficiency and crop yield; however, its microbial mechanism involved remains unclear. This study aimed to explore the temporal impact of peanut introduction on microorganisms related to nitrogen metabolism in rotation systems. In this study, the dynamics of diazotrophic communities in two crop seasons and wheat yields of two rotation systems: winter wheat - summer maize (WM) and spring peanut → winter wheat - summer maize (PWM) in the North China Plain were investigated. Our results showed that peanut introduction increased wheat yield and biomass by 11.6% (p < 0.05) and 8.9%, respectively. Lower Chao1 and Shannon indexes of the diazotrophic communities were detected in soils that sampling in June compared with those sampling in September, although no difference was found between WM and PWM. Principal co-ordinates analysis (PCoA) showed that rotation system significantly changed the diazotrophic community structures (PERMANOVA; p < 0.05). Compared with WM, the genera of Azotobacter, Skermanella, Azohydromonas, Rhodomicrobium, Azospirillum, Unclassified_f_Opitutaceae, and Unclassified_f_Rhodospirillaceae were significantly enriched (p < 0.05) in PWM. Furthermore, rotation system and sampling time significantly influenced soil properties, which significantly correlated with the top 15 genera in relative abundance. Partial least squares path modeling (PLS-PM) analysis further showed that the diazotrophic community diversity (alpha- and beta-diversity) and soil properties (pH, SOC and TN) significantly affected wheat yield. In conclusion, legume inclusion has the potential to stabilize diazotrophic community structure at the temporal scales and increase subsequent crop yield.

Uncovering the processes of microbial community assembly in the near-surface sediments of a climate-sensitive glacier-fed lake

Glacier-fed lakes are characterized by cold temperatures, high altitudes, and nutrient-poor conditions. Despite these challenging conditions, near-surface sediments of glacier-fed lakes harbor rich microbial communities that are critical for ecosystem functioning and serve as a bridge between aquatic ecology and the deep subsurface biosphere. However, there is limited knowledge regarding the microbial communities and their assembly processes in these sediments, which are highly vulnerable to climate change. To fill this knowledge gap, this study systematically analyzed environmental variables, microbial communities, diversity, co-occurrence relationships, and community assembly processes in the near-surface sediments of a glacier-fed lake in the Tibetan Plateau. The results revealed distinct vertical gradients in microbial diversity and subcommunities, highlighting the significant influence of selection processes and adaptive abilities on microbial communities. Specifically, specialists played a crucial role within the overall microbial communities. Microbial assembly was primarily driven by homogeneous selection, but its influence declined with increasing depth. In contrast, homogenizing dispersal showed an opposite pattern, and the bottom layer exhibited heterogeneous selection and undominated processes. These patterns of microbial assembly were primarily driven by environmental gradients, with significant contributions from processes associated to ammonium and organic matter deposition, as well as chemical precipitation in response to a warming climate. This study enhances our understanding of the microbial communities and assembly processes in the near-surface sediments of glacier-fed lakes and sheds light on geo-microbiological processes in climate-sensitive lacustrine sediments.

The cultivation regimes of Morchella sextelata trigger shifts in the community assemblage and ecological traits of soil bacteria

The successful large-scale cultivation of morel mushrooms (Morchella sextelata) requires a comprehensive understanding of the soil bacterial communities associated with morel-farming beds, as the interactions between fungi and bacteria play a crucial role in shaping the soil microbiome. In this study, we investigated the temporal distribution and ecological characteristics of soil bacteria associated with morel fruiting bodies at different stages, specifically the conidial and primordial stages, under two cropping regimes, non-continuous cropping (NCC) and continuous cropping (CC). Our findings revealed a significant reduction in the yield of morel primordia during the third year following 2 years of CC (0.29 ± 0.25 primordia/grid), in comparison to the NCC regime (12.39 ± 6.09 primordia/grid). Furthermore, inoculation with morel mycelia had a notable impact on soil bacterial diversity, decreasing it in the NCC regime and increasing the number of generalist bacterial members in the CC regime. The latter regime also led to the accumulation of nutrients in the soil beds, resulting in a shift from a stochastic to a deterministic process in the composition of the bacterial community, which differed from the NCC regime. Additionally, mycelial inoculation had a positive effect on the abundance of potential copiotrophic/denitrifying and N-fixing bacteria while decreasing the abundance of oligotrophic/nitrifying bacteria. Interestingly, this effect was more pronounced in the NCC regime than in the CC regime. These results suggest that the increase in potential copiotrophic/denitrifying and N-fixing bacteria facilitated the decomposition of nutrients in exogenous nutrient bags by morel mushrooms, thereby maintaining nitrogen balance in the soil. Overall, our study provides valuable insights into the interactions between morel mycelia and the associated soil bacteriome as well as the influence of different cultivation regimes on these interactions. These findings contribute to our understanding of the complex dynamics of the soil microbiome and can inform strategies for optimizing morel mushroom cultivation.

Eucommia ulmoides Oliver repairs the disorder of intestinal microflora caused by high starch in Micropterus salmoides and improves resistance to pathogens

Eucommia ulmoides Oliver (EuO) is a natural medicine that can improve the composition of intestinal flora in fish, but more experiments and data are needed to support whether it can effectively improve the changes of intestinal flora and intestinal damage caused by high starch. This study examined the changes in intestinal structure as well as intestinal flora before and after the addition of EuO to high-starch diets and analyzed the effects of such changes on immune and digestive functions. The results showed that EuO reduces mortality during Nocardia seriolae attack and can reduce starch-induced intestinal inflammation. Eucommia ulmoides Oliver supplementation was able to alter the changes of intestinal flora in fatty acid degradation, bacterial chemotaxis, porphyrin metabolism and flagella assembly caused by high starch. By analyzing the abundance and correlation of bacterial communities, three bacterial communities that were significantly related to the intervention effect of EuO were screened. Further analysis revealed that EuO supplementation reduced the increase in abundance of Limnochordaceae, Nitrolancea, Lysinibacillus, and Hydrogenispora induced by high starch, which were negatively correlated with levels of the immunoreactive substance LZM in fish. This study reveals the regulatory effects of EuO on the intestinal flora of Micropterus salmoides fed on high starch diets, and provides a theoretical basis for reducing starch damage to fish in production.

Distinct prokaryotic and eukaryotic communities and networks in two agricultural fields of central Japan with different histories of maize-cabbage rotation

Crop rotation is an important agricultural practice for homeostatic crop cultivation. Here, we applied high-throughput sequencing of ribosomal RNA gene amplicons to investigate soil biota in two fields of central Japan with different histories of maize-cabbage rotation. We identified 3086 eukaryotic and 17,069 prokaryotic sequence variants (SVs) from soil samples from two fields rotating two crops at three different growth stages. The eukaryotic and prokaryotic communities in the four sample groups of two crops and two fields were clearly distinguished using β-diversity analysis. Redundancy analysis showed the relationships of the communities in the fields to pH and nutrient, humus, and/or water content. The complexity of eukaryotic and prokaryotic networks was apparently higher in the cabbage-cultivated soils than those in the maize-cultivated soils. The node SVs (nSVs) of the networks were mainly derived from two eukaryotic phyla: Ascomycota and Cercozoa, and four prokaryotic phyla: Pseudomonadota, Acidobacteriota, Actinomycetota, and Gemmatimonadota. The networks were complexed by cropping from maize to cabbage, suggesting the formation of a flexible network under crop rotation. Ten out of the 16 eukaryotic nSVs were specifically found in the cabbage-cultivated soils were derived from protists, indicating the potential contribution of protists to the formation of complex eukaryotic networks.

More Than the Sum of Its Parts: Unlocking the Power of Network Structure for Understanding Organization and Function in Microbiomes

Plant and soil microbiomes are integral to the health and productivity of plants and ecosystems, yet researchers struggle to identify microbiome characteristics important for providing beneficial outcomes. Network analysis offers a shift in analytical framework beyond "who is present" to the organization or patterns of coexistence between microbes within the microbiome. Because microbial phenotypes are often significantly impacted by coexisting populations, patterns of coexistence within microbiomes are likely to be especially important in predicting functional outcomes. Here, we provide an overview of the how and why of network analysis in microbiome research, highlighting the ways in which network analyses have provided novel insights into microbiome organization and functional capacities, the diverse network roles of different microbial populations, and the eco-evolutionary dynamics of plant and soil microbiomes.

Pathogen resistance in soils associated with bacteriome network reconstruction through reductive soil disinfestation

Reductive soil disinfestation (RSD) is an effective bioremediation technique to restructure the soil microbial community and eliminate soilborne phytopathogens. Yet we still lack a comprehensive understanding of the keystone taxa involved and their roles in ecosystem functioning in degraded soils treated by RSD. In this study, the bacteriome network structure in RSD-treated soil and the subsequent cultivation process were explored. As a result, bacterial communities in RSD-treated soil developed more complex topologies and stable co-occurrence patterns. The richness and diversity of keystone taxa were higher in the RSD group (module hub: 0.57%; connector: 23.98%) than in the Control group (module hub: 0.16%; connector: 19.34%). The restoration of keystone taxa in RSD-treated soil was significantly (P < 0.01) correlated with soil pH, total organic carbon, and total nitrogen. Moreover, a strong negative correlation (r =  -0.712; P < 0.01) was found between keystone taxa richness and Fusarium abundance. Our results suggest that keystone taxa involved in the RSD network structure are capable of maintaining a flexible generalist mode of metabolism, namely with respect to nitrogen fixation, methylotrophy, and methanotrophy. Furthermore, distinct network modules composed by numerous anti-pathogen agents were formed in RSD-treated soil; i.e., the genera Hydrogenispora, Azotobacter, Sphingomonas, and Clostridium_8 under the soil treatment stage, and the genera Anaerolinea and Pseudarthrobacter under the plant cultivation stage. The study provides novel insights into the association between fungistasis and keystone or sensitive taxa in RSD-treated soil, with significant implications for comprehending the mechanisms of RSD. KEY POINTS: • RSD enhanced bacteriome network stability and restored keystone taxa. • Keystone taxa richness was negatively correlated with Fusarium abundance. • Distinct sensitive OTUs and modules were formed in RSD soil.

Impact of conservation tillage on wheat performance and its microbiome

Winter wheat is an important cereal consumed worldwide. However, current management practices involving chemical fertilizers, irrigation, and intensive tillage may have negative impacts on the environment. Conservation agriculture is often presented as a sustainable alternative to maintain wheat production, favoring the beneficial microbiome. Here, we evaluated the impact of different water regimes (rainfed and irrigated), fertilization levels (half and full fertilization), and tillage practices (occasional tillage and no-tillage) on wheat performance, microbial activity, and rhizosphere- and root-associated microbial communities of four winter wheat genotypes (Antequera, Allez-y, Apache, and Cellule) grown in a field experiment. Wheat performance (i.e., yield, plant nitrogen concentrations, and total nitrogen uptake) was mainly affected by irrigation, fertilization, and genotype, whereas microbial activity (i.e., protease and alkaline phosphatase activities) was affected by irrigation. Amplicon sequencing data revealed that habitat (rhizosphere vs. root) was the main factor shaping microbial communities and confirmed that the selection of endophytic microbial communities takes place thanks to specific plant-microbiome interactions. Among the experimental factors applied, the interaction of irrigation and tillage influenced rhizosphere- and root-associated microbiomes. The findings presented in this work make it possible to link agricultural practices to microbial communities, paving the way for better monitoring of these microorganisms in the context of agroecosystem sustainability.